Evidence map›Paper›PMID 39117654›Full record

ArticleNature communications2024

Transcriptomic classification of diffuse large B-cell lymphoma identifies a high-risk activated B-cell-like subpopulation with targetable MYC dysregulation.

Matthew E Stokes, Kerstin Wenzl, C Chris Huang, María Ortiz, Chih-Chao Hsu, Matthew J Maurer, Nicholas Stong, Yumi Nakayama, Lei Wu, Hsiling Chiu and 18 more

Abstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. Review
  4. Article
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  6. Review
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  8. Review
  9. Article
  10. Interferon Epsilon Loss Is Elusive 9p21 Link to Immune-Cold Tumors, Resistant to Immune Checkpoint Therapy, and Endogenous CXCL9/10 Induction.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2025
    Review
  11. Article
  12. Article
  13. Evaluation of Etiologic Heterogeneity for Risk of Diffuse Large B-Cell Lymphoma Subtype Defined by the Cell of Origin.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2025
    Article
  14. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

28 authors.

Matthew E StokesInformatics and Predictive Sciences, Bristol Myers Squibb, Summit, NJ, USA.
Kerstin WenzlDivision of Hematology, Mayo Clinic, Rochester, MN, USA.
C Chris HuangTranslational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA.ORCID 0000-0002-1116-2756
María OrtizInformatics and Predictive Sciences, Bristol Myers Squibb, Seville, Spain.
Chih-Chao HsuTranslational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA.
Matthew J MaurerDepartment of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.ORCID 0000-0002-1867-0526
Nicholas StongInformatics and Predictive Sciences, Bristol Myers Squibb, Summit, NJ, USA.ORCID 0000-0002-0678-637X
Yumi NakayamaTranslational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA.ORCID 0000-0003-1279-1519
Lei WuTranslational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA.
Hsiling ChiuTranslational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA.ORCID 0000-0003-1390-0553
Ann PolonskaiaTranslational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA.
Samuel A DanzigerBMS at the time the study was conducted, Amazon, Seattle, WA, USA.
Fadi TowficBMS at the time the study was conducted, Prometheus Biosciences, San Diego, CA, USA.
Joel ParkerLifeEDIT Therapeutics, Research Triangle Park, Durham, NC, USA.
Rebecca L KingDivision of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
Brian K LinkDivision of Hematology, Oncology, Blood and Marrow Transplant, University of Iowa, Iowa City, IA, USA.
Susan L SlagerDivision of Hematology, Mayo Clinic, Rochester, MN, USA.ORCID 0000-0002-5173-4712
Vivekananda SarangiDivision of Hematology, Mayo Clinic, Rochester, MN, USA.
Yan W AsmannDepartment of Health Science Research, Mayo Clinic, Jacksonville, FL, USA.
Joseph P NovakDivision of Hematology, Mayo Clinic, Rochester, MN, USA.
Akshay SudhindraClinical Research and Development, Bristol Myers Squibb, Summit, NJ, USA.
Stephen M AnsellDivision of Hematology, Mayo Clinic, Rochester, MN, USA.ORCID 0000-0003-1244-6758
Thomas M HabermannDivision of Hematology, Mayo Clinic, Rochester, MN, USA.ORCID 0000-0003-3532-9132
Patrick R HagnerTranslational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA.
Grzegorz S NowakowskiDivision of Hematology, Mayo Clinic, Rochester, MN, USA.
James R CerhanDivision of Hematology, Mayo Clinic, Rochester, MN, USA.ORCID 0000-0002-7482-178X
Anne J Novak *Division of Hematology, Mayo Clinic, Rochester, MN, USA.ORCID 0000-0002-7904-1651
Anita K Gandhi *Translational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA. anita.gandhi@bms.com.

Funding

Viral VectorP30CA086862 · NCI · UNIVERSITY OF IOWA · PI Christopher K Laubenthal · 2000 to 2026
$70.0M
The Role of Monocytes in non-Hodgkin LymphomaP50CA097274 · NCI · UNIVERSITY OF IOWA · PI LENTZ, STEVEN R · 2002 to 2021
$45.7M
The Lymphoma Epidemiology of Outcomes (LEO) Cohort Study (Supplement)U01CA195568 · NCI · MAYO CLINIC ROCHESTER · PI CERHAN, JAMES R, FLOWERS, CHRISTOPHER R · 2015 to 2025
$22.1M
Genetic Predictors of Early Clinical Failure in Diffuse Large B Cell LymphomaR01CA212162 · NCI · MAYO CLINIC ROCHESTER · PI CERHAN, JAMES R, NOVAK, ANNE JOSEPHINE · 2017 to 2021
$3.3M
Trace elements among Iowa pesticide applicatorsR03CA099524 · NCI · UNIVERSITY OF IOWA · PI DENNIS, LESLIE K · 2003 to 2004
$148k
NCI NIH HHS P30 CA086862NCI NIH HHS P50 CA097274NCI NIH HHS R01 CA212162NCI NIH HHS R03 CA099524NCI NIH HHS U01 CA195568U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) CA195568U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) CA212162-01A1U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) CA97274
6 · The paper itself

Abstract

Immunochemotherapy has been the mainstay of treatment for newly diagnosed diffuse large B-cell lymphoma (ndDLBCL) yet is inadequate for many patients. In this work, we perform unsupervised clustering on transcriptomic features from a large cohort of ndDLBCL patients and identify seven clusters, one called A7 with poor prognosis, and develop a classifier to identify these clusters in independent ndDLBCL cohorts. This high-risk cluster is enriched for activated B-cell cell-of-origin, low immune infiltration, high MYC expression, and copy number aberrations. We compare and contrast our methodology with recent DLBCL classifiers to contextualize our clusters and show improved prognostic utility. Finally, using pre-clinical models, we demonstrate a mechanistic rationale for IKZF1/3 degraders such as lenalidomide to overcome the low immune infiltration phenotype of A7 by inducing T-cell trafficking into tumors and upregulating MHC I and II on tumor cells, and demonstrate that TCF4 is an important regulator of MYC-related biology in A7.

Indexed as

Gene Expression Regulation, NeoplasticIkaros Transcription FactorLenalidomideLymphoma, Large B-Cell, DiffuseProto-Oncogene Proteins c-mycTranscription Factor 4TranscriptomeAnimalsB-LymphocytesCell Line, TumorDNA Copy Number VariationsGene Expression ProfilingHumansMicePrognosisT-LymphocytesIkaros Transcription FactorIKZF1 protein, humanIKZF3 protein, humanLenalidomideMYC protein, humanProto-Oncogene Proteins c-mycTCF4 protein, humanTranscription Factor 4

Identifiers

PMID39117654
PMCPMC11310352

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.